verify.dump¶
Run the experiments of a project and store what they produce, verify dump.
Bases: TypedDict
Everything dump stores of the experiments of a model.
Serialize the attributes of an object (a figure) into json values.
References back to the experiment and to parents are replaced by their type, so that the specification of a figure only contains the figure.
Get the metadata of a fit mapping as {field: name}.
Enum members are stored by name, so a change of their values or of the enum
type (StrEnum) does not count as a change.
Describe a fit mapping by its data, its observable, weight and metadata.
Get the range of the x values of the data and of the simulation of a mapping.
The data are converted into the unit of the simulation.
Get a simulation with a common fixed output grid (dump --grid).
The output times are n + 1 equidistant times from the start to the end
of the simulation and the times of its changes (and of the dimensions of a
scan with a time), in the time unit of the simulation; the steps or times
of the simulation are replaced, everything else stays. The output of the
integrator differs between two runs whose model or tolerances differ;
on this grid both dumps of a compare have the same times, which are
matched exactly, without interpolation, so a compare resolves its
threshold (a migration compare dumps both models with --grid).
A scan has its simulation on the grid and every simulation of a dimension of simulations, each on the grid of its own start, end and changes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
simulation
|
Simulation | Scan
|
the simulation or the scan. |
required |
n
|
int
|
the number of intervals of the grid. |
required |
Returns:
| Type | Description |
|---|---|
Simulation | Scan
|
The simulation or the scan on the grid, a new object. |
Raises:
| Type | Description |
|---|---|
ValueError
|
for an object which is no simulation or scan, or a time which is a quantity of a simulation without a time unit. |
Get the experiments defined in the modules of the experiments of a project.
Every subclass of SimulationExperiment defined in the modules of the
project (CheckSettings.experiment_modules below its package) counts,
except the classes from which another found class derives (the base
experiments), see sbmlsim.project_checks.defined_experiments.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
project
|
Project
|
the project. |
required |
errors
|
dict[str, str]
|
the traceback of every module which does not import is added
here, as |
required |
Returns:
| Type | Description |
|---|---|
list[type[SimulationExperiment]]
|
The experiment classes in the order of module name and definition. |
Get the variant of the model a task of an experiment runs on.
The experiment decides (SimulationExperiment.variant_of, the hook of a
framework which builds a model per group of subjects); else the variant of
the project whose file is the source of the model of the task; None for a
model which is none of the variants.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
project
|
Project
|
the project. |
required |
experiment
|
SimulationExperiment
|
the experiment, initialized. |
required |
task
|
str
|
the key of the task. |
required |
Returns:
| Type | Description |
|---|---|
str | None
|
The name of the variant, or |
Get the versions of the packages which make a dump.
sbmlsim, the distribution of the package of the project and, for a project
with release settings, the libraries of the release (core_libraries) which
are installed.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
project
|
Project
|
the project. |
required |
Returns:
| Type | Description |
|---|---|
dict[str, str]
|
The version by name of the distribution. |
Run the experiments of a project and store everything in a pickle.
Returns:
| Type | Description |
|---|---|
int
|
1 if an experiment failed, else 0. |
Raises:
| Type | Description |
|---|---|
UsageError
|
for an unknown experiment or tolerance, or a project without experiments. |
Store the results, datasets, fit mappings and figures of a run experiment.
The time of a grid is a coordinate of a result; it is stored as the
variable time over ("time",), which the comparison reads. The variant of
the build of every task is stored (builds, see variant_of), so that a
study which moves to the build of another variant is a difference of its
own.
Get the specification of a figure, its attributes as json.
RESOLVED adds the settings of the experiment and of the figure (the
figure_settings of the experiment overridden by the settings of the
figure) and the width and height the figure is rendered with, as sbmlsim
resolves them without the settings of a run, so that compare sees a change
of a setting of the experiment or of the size of the panels.